Contents

3D Head Visualizations

Topographic map in 3D head

from simpl_eeg import topomap_3d_head, eeg_objects

import warnings
warnings.filterwarnings('ignore')

Note

Please include the line below in your IDE so that the changes would be simultaneously reflected when you make a change to the python scripts.

%load_ext autoreload

%autoreload 2

Define parameters

A detailed description of all parameters can be found in the topomap_3d_head.animate_3d_head docstring:

help(topomap_3d_head.animate_3d_head)

Help on function animate_3d_head in module simpl_eeg.topomap_3d_head:

animate_3d_head(epoch, plot_title='', color_title='EEG MicroVolt', color_min=-50, color_max=50, colormap='Bluered')
    Plot an animated topographic map in a 3D head shape
    
    Args:
        epoch (mne.epochs.Epochs): An epoched file for the EEGLab data
        plot_title (str, optionl): The title of the plot. Defaults to "".
        color_title (str,  optional): The title of the color bar. Defaults to "EEG MicroVolt".
        color_min (int, optional): The minimum EEG voltage value to be shown on the color bar. Defaults to -50.
        color_max (int, optional): The maximum EEG voltage value to be shown on the color bar. Defaults to 50.
        colormap (str, optional): The colour scheme to use. Defaults to Bluered.
    
    Returns:
        figure: An animated topographic map in a 3D head shape

# change values below to values of interest

experiment_folder = "../../data/927"
nth_epoch = 0

color_min = -40
color_max = 40
colormap = "RdBu_r"
time_stamp = -300

Create epoched data

For additional options see Creating EEG Objects section.

epochs = eeg_objects.Epochs(experiment_folder)
epoch = epochs.get_nth_epoch(nth_epoch)

Reading /Users/sasha/mds/simpl_eeg_capstone/data/927/fixica.fdt

Not setting metadata

Not setting metadata

33 matching events found

Setting baseline interval to [-0.2998046875, 0.0] sec

Applying baseline correction (mode: mean)

0 projection items activated

Loading data for 33 events and 2049 original time points ...

0 bad epochs dropped

Create the topographic map in 3D head shape

topo_3d__head_static = topomap_3d_head.topo_3d_map(
    epoch,
    time_stamp,
    color_title="EEG MicroVolt",
    color_min=color_min,
    color_max=color_max,
    colormap=colormap,
)

topo_3d__head_static.show()

Generating the animation

topo_3d_head = topomap_3d_head.animate_3d_head(
    epoch,
    color_title="EEG MicroVolt",
    color_min=color_min,
    color_max=color_max,
    colormap=colormap,
)

topo_3d_head.show()

Saving the animation

Save static plot
static_file_path = "../../exports/examples/topo_3d_static.svg"  # change the file path to where you would like to save the file

topo_3d__head_static.write_image(static_file_path, engine="kaleido")

static_file_path_png = "../../exports/examples/topo_3d_static.png"  # change the file path to where you would like to save the file

topo_3d__head_static.write_image(static_file_path_png) # no need to specify engine if not saved as svg file
Save animation as html
html_file_path = "../../exports/examples/topo_3d.html"  # change the file path to where you would like to save the file

topo_3d_head.write_html(html_file_path)
Save animation as gif
topomap_3d_head.save_gif(epoch, gifname="topo_3d_head_ani", duration=200)
Save animation as mp4

Note

You need to save the file as gif first and then convert it into mp4 file.

import moviepy.editor as mp

clip = mp.VideoFileClip("topo_3d_head_ani.gif")  # change the file path to where you saved the gif file
clip.write_videofile("../../exports/examples/topo_3d_head_ani.mp4")  # change the file path to where you would like to save the file
3D Brain Visualizations User Interface